COPASI software for modeling and simulation of biochemical networks

描述（由申请人提供）：生化网络的建模和模拟已经成为帮助理解细胞行为和促进现代实验定量解释的基本活动。一种新的方法“系统生物学”正在被提倡，它结合了建模、模拟和定量实验。生物医学研究越来越依赖于计算模型的构建和模拟。可以说，随着个性化医疗的发展，这种情况将更加明显。然而，建模和仿真的技术方面对大量生物医学研究人员来说是压倒性的，所需要的是一个软件应用程序，能够提供适当的数值算法，由用户界面屏蔽，帮助生物医学研究人员进行所需的模拟。我们建议通过继续开发我们的软件COPASI来解决这一需求，该软件已经在研究界广泛使用。该项目还将向COPASI活跃的用户/生物医学研究人员社区提供支持。我们将通过以下具体目标来解决这个问题：目标1：通过增加对包含噪声和显式时间延迟的模型的支持，使COPASI具有新功能，以提供高级模型功能。将实现对1和2维隔室（细丝和膜）的支持，以及对随机和延迟微分模拟算法中的离散事件的支持。目标2。改进和扩展互操作性和标准遵从性。COPASI将能够方便用户以SED-ML格式创建和读取仿真信息，能够以SBRML格式保存和读取仿真和实验结果，并支持拟议的SBML Level 3。目标3。软件维护。现有的测试计划将继续和扩大，包括设计适当的收集模型，以测试软件的各种功能；Bug报告将被收集和修复；将从用户处收集改进建议并贯彻执行。目标4。支持建模社区。将开发和维护在线支持，如视频教程、用户论坛、用户手册和常见问题。COPASI用户讲习班将每年举行一次。

DESCRIPTION (provided by applicant): Modeling and simulation of biochemical networks has become an essential activity to aid in the understanding of cellular behavior and to facilitate quantitative interpretation of modern experiments. A new approach, "systems biology", is being advocated which combines modeling, simulation and quantitative experiments. Biomedical research is becoming increasingly dependent on construction and simulation of computational models. Arguably this will be even more the case with the development of personalized medicine. However, the technical aspects of modeling and simulation are overwhelming to a large number of biomedical researchers, and what is needed is a software application that is capable of providing the appropriate numerical algorithms shielded by a user interface that aides the biomedical researcher to conduct the required simulations. We propose to address this need with continuing development of our software COPASI, which is already widely used in the research community. This project will also provide support to the vibrant community of COPASI users/biomedical researchers. We will address this with the following Specific Aims: Aim 1: Enable COPASI with new functionality to provide advanced model capabilities by adding support for models containing noise and explicit time delays. Support for 1 and 2 dimensional compartments (filaments and membranes) will be implementes as well as support for discrete events in stochastic and delay differential simulation algorithms. Aim 2. Improve and extend interoperability and standards compliance. COPASI will be equipped to facilitate users to create and read simulation information in SED-ML format, it will be enabled to save and read simulation and experimental result in the SBRML format, and it will support the proposed SBML Level 3. Aim 3. Software maintenance. An existing testing plan will be continued and expanded, including appropriate collection models designed to test the various functions of the software; bug reports will be collected and fixed; suggestions for improvement will be collected from users and followed through. Aim 4. Support the modeling community. Online support will be developed and maintained, such as video tutorials, user forum, user manual, and frequently asked questions. A COPASI User's Workshop will be held annually.